research-article

Accelerating multiple target drug screening on GPUs

Authors:

Irene Sánchez-Linares,

Horacio Pérez-Sánchez,

Ginés D. Guerrero,

José M. Cecilia,

José M. GarcíaAuthors Info & Claims

CMSB '11: Proceedings of the 9th International Conference on Computational Methods in Systems Biology

Pages 95 - 102

https://doi.org/10.1145/2037509.2037523

Published: 21 September 2011 Publication History

Abstract

The completion of the human genome project has brought new and still unprocessed information about potential targets for the treatment of human diseases with drugs. The efficacy of a drug can be vastly improved through the interaction with multiple targets, although undesirable side effects must also be studied. Experimental approaches for this purpose are very expensive and time consuming, while in-silico approaches can efficiently propose accurate predictions that drastically reduce testing procedures in the laboratory. Nevertheless, in-silico approaches for multiple target identification have not been yet fully explored and most of them still deal with rigid receptor models. It has been shown recently that the docking program FlexScreen includes efficiently protein flexibility. However, processing large databases of target proteins is a very time consuming process. In a new optimization approach, massively parallel architectures like GPUs can greatly overcome these limitations. In this study we report our FlexScreen parallelization efforts using CUDA.

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Cited By

Pérez-Sánchez HRezaei VMezhuyev VMan DPeña-García Jden-Haan HGesing S(2016)Developing science gateways for drug discovery in a grid environmentSpringerPlus10.1186/s40064-016-2914-x5:1Online publication date: 9-Aug-2016
https://doi.org/10.1186/s40064-016-2914-x
Jaghoori MBleijlevens BOlabarriaga S(2016)1001 Ways to run AutoDock Vina for virtual screeningJournal of Computer-Aided Molecular Design10.1007/s10822-016-9900-930:3(237-249)Online publication date: 20-Feb-2016
https://doi.org/10.1007/s10822-016-9900-9
Jaghoori Mvan Altena ABleijlevens BRamezani SFont JOlabarriaga S(2015)A multi‐infrastructure gateway for virtual drug screeningConcurrency and Computation: Practice and Experience10.1002/cpe.349827:16(4478-4490)Online publication date: 21-May-2015
https://doi.org/10.1002/cpe.3498
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Accelerating multiple target drug screening on GPUs

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cover image ACM Other conferences

CMSB '11: Proceedings of the 9th International Conference on Computational Methods in Systems Biology

September 2011

224 pages

ISBN:9781450308175

DOI:10.1145/2037509

Conference Chair:
François Fages
INRIA Paris-Rocquencourt, France

Copyright © 2011 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

Sponsors

TCSIM: IEEE Computer Society Technical Committee on Simulation
University Henri-Poincare: University Henri-Poincare - France
NVIDIA
CNRS: Centre National De La Rechercue Scientifique
Microsoft Research: Microsoft Research

In-Cooperation

SIGBio: ACM Special Interest Group on Bioinformatics

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 21 September 2011

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Fundación Séeneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia)
Federación Española de Enfermedades Raras

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CMSB'11

Sponsor:

TCSIM
University Henri-Poincare
CNRS
Microsoft Research

CMSB'11: 9th International Conference on Computational Methods in Systems Biology

September 21 - 23, 2011

Paris, France

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Cited By

Pérez-Sánchez HRezaei VMezhuyev VMan DPeña-García Jden-Haan HGesing S(2016)Developing science gateways for drug discovery in a grid environmentSpringerPlus10.1186/s40064-016-2914-x5:1Online publication date: 9-Aug-2016
https://doi.org/10.1186/s40064-016-2914-x
Jaghoori MBleijlevens BOlabarriaga S(2016)1001 Ways to run AutoDock Vina for virtual screeningJournal of Computer-Aided Molecular Design10.1007/s10822-016-9900-930:3(237-249)Online publication date: 20-Feb-2016
https://doi.org/10.1007/s10822-016-9900-9
Jaghoori Mvan Altena ABleijlevens BRamezani SFont JOlabarriaga S(2015)A multi‐infrastructure gateway for virtual drug screeningConcurrency and Computation: Practice and Experience10.1002/cpe.349827:16(4478-4490)Online publication date: 21-May-2015
https://doi.org/10.1002/cpe.3498
Ellingson SDakshanamurthy SBrown MSmith JBaudry J(2014)Accelerating virtual high-throughput ligand dockingConcurrency and Computation: Practice & Experience10.1002/cpe.307026:6(1268-1277)Online publication date: 25-Apr-2014
https://dl.acm.org/doi/10.1002/cpe.3070
Perez-Sanchez HGuerrero GGarcia JPena JCecilia JCano GOrts-Escolano SGarcia-Rodriguez J(2013)Improving drug discovery using a neural networks based parallel scoring functionThe 2013 International Joint Conference on Neural Networks (IJCNN)10.1109/IJCNN.2013.6706909(1-5)Online publication date: Aug-2013
https://doi.org/10.1109/IJCNN.2013.6706909
Sánchez-Linares IPérez-Sánchez HCecilia JGarcía J(2012)High-Throughput parallel blind Virtual Screening using BINDSURFBMC Bioinformatics10.1186/1471-2105-13-S14-S1313:S14Online publication date: 7-Sep-2012
https://doi.org/10.1186/1471-2105-13-S14-S13
Guerrero GPerez-Sánchez HCecilia JGarcia J(2012)Parallelization of Virtual Screening in Drug Discovery on Massively Parallel ArchitecturesProceedings of the 2012 20th Euromicro International Conference on Parallel, Distributed and Network-based Processing10.1109/PDP.2012.26(588-595)Online publication date: 15-Feb-2012
https://dl.acm.org/doi/10.1109/PDP.2012.26

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